Add Gao-Her-DUF system

README.md

@@ -20,21 +20,21 @@ METPO source class and (optionally) to literature evidence.
 | PHYSIOLOGY | 45 | 48 | 0 | 50 | 94 |
 | ENVIRONMENT | 121 | 0 | 0 | 121 | 122 |
 | ECOLOGY | 26 | 0 | 0 | 26 | 26 |
-| GENOMICS | 19 | 152 | 0 | 171 | 171 |
+| GENOMICS | 19 | 153 | 0 | 172 | 172 |
 | UPPER | 8 | 0 | 0 | 5 | 8 |
 | METABOLISM | 120 | 36 | 23 | 50 | 180 |
 | OBSERVATION | 0 | 0 | 20 | 0 | 20 |
 | QUANTITATIVE_PROPERTY | 0 | 0 | 7 | 0 | 7 |
 | OTHER | 0 | 1 | 0 | 0 | 32 |
-| **TOTAL** | **427** | **240** | **50** | **511** | **755** |
+| **TOTAL** | **427** | **241** | **50** | **512** | **756** |
 
 477 records have a terminal curation status: 427 are `REVIEWED` and 50 are
 `DEPRECATED`; three morphology records, 36 newer metabolism records,
-forty-eight physiology records, 152 genomics records, and one other
+forty-eight physiology records, 153 genomics records, and one other
 record are `PROPOSED`, and thirty-eight records are still `SEEDED` (one
 environment, one metabolism, four morphology, one physiology, and thirty-one
 other).
-Across the corpus, 511 records currently carry causal graphs. The 50 deprecated
+Across the corpus, 512 records currently carry causal graphs. The 50 deprecated
 records (23
 metabolism, 20 observation, 7 quantitative_property) are generic relation or
 measurement carriers from the upstream METPO seed that are not intended to carry
@@ -92,7 +92,7 @@ TraitMech/
 ├── data/
 │   ├── raw/metpo.owl                    # vendored METPO release (2026-06-12)
 │   ├── embeddings/                      # graph, nearest-neighbour, and UMAP data
-│   └── traits/<category>/<slug>.yaml    # 755 curated TraitRecords
+│   └── traits/<category>/<slug>.yaml    # 756 curated TraitRecords
 ├── mappings/                                # reviewed node and predicate groundings
 ├── research/traits/                         # source-finding reports and sidecars
 ├── proposals/                               # upstream METPO proposal cohorts

app/dashboard/priority.html

@@ -1,8 +1,8 @@
 <!doctype html><meta charset=utf-8><title>TraitMech curation priority</title><style>body{font:14px/1.5 system-ui,sans-serif;margin:2rem;max-width:1200px}table{border-collapse:collapse;width:100%}th,td{padding:.35rem .5rem;border-bottom:1px solid #ddd;text-align:left;vertical-align:top}th{background:#f4f4f4}code{font-size:.9em}.a{font-weight:600}tr:hover{background:#fafafa}.n{text-align:right}figure{margin:0 0 1.5rem}figcaption{color:#555}</style>
 <h1>TraitMech curation priority</h1>
-<figure><figcaption>755 records; 109 not mechanism records, 20 deprecated &mdash; both scored to the floor rather than dropped silently.</figcaption></figure>
-<p><strong>Research.</strong> 278 mechanism record(s) have no artifact; the rest need existing research applied, not re-run.</p>
-<ul><li><code>DROP_NON_MECHANISM</code> &mdash; 109</li><li><code>DROP_DEPRECATED</code> &mdash; 20</li><li><code>CURATE_ROOT_WITH_SUBTYPES</code> &mdash; 4</li><li><code>ADD_CANONICAL_EXAMPLES</code> &mdash; 92</li><li><code>BUILD_CAUSAL_GRAPH</code> &mdash; 119</li><li><code>DEEPEN_CAUSAL_GRAPH</code> &mdash; 195</li><li><code>ALREADY_DEEP</code> &mdash; 59</li><li><code>CURATE_ROOT</code> &mdash; 157</li></ul>
+<figure><figcaption>756 records; 109 not mechanism records, 20 deprecated &mdash; both scored to the floor rather than dropped silently.</figcaption></figure>
+<p><strong>Research.</strong> 279 mechanism record(s) have no artifact; the rest need existing research applied, not re-run.</p>
+<ul><li><code>DROP_NON_MECHANISM</code> &mdash; 109</li><li><code>DROP_DEPRECATED</code> &mdash; 20</li><li><code>CURATE_ROOT_WITH_SUBTYPES</code> &mdash; 4</li><li><code>ADD_CANONICAL_EXAMPLES</code> &mdash; 93</li><li><code>BUILD_CAUSAL_GRAPH</code> &mdash; 119</li><li><code>DEEPEN_CAUSAL_GRAPH</code> &mdash; 195</li><li><code>ALREADY_DEEP</code> &mdash; 59</li><li><code>CURATE_ROOT</code> &mdash; 157</li></ul>
 <p><strong>Lumping.</strong> 10 binned series detected; 112 sibling pairs have mean node-label overlap <strong>0.069</strong> (max 0.188); 51 direct child/parent pairs have mean overlap 0.085 (max 0.214). Only 2 of 463 child edges share the same subject/predicate/object structure with a parent. The unweighted mean of family means is 0.068 against a lump threshold of 0.6. Nothing lumps, because the bins carry distinct mechanism content &mdash; the rule DisMech applies to MONDO subtype series does not transfer unretuned.</p>
 <h2>Top 80</h2>
 <table><tr><th class=n>score</th><th>action</th><th>trait</th><th class=n>edges</th><th class=n>cmp</th><th class=n>orph</th><th class=n>ex</th><th>series</th><th>why</th></tr>

app/dashboard/priority.json

@@ -1,6 +1,6 @@
 {
   "meta": {
-    "records": 755,
+    "records": 756,
     "series_families": 10,
     "excluded_non_mechanism": 109,
     "excluded_deprecated": 20,
@@ -14,14 +14,14 @@
     "child_edges_compared": 463,
     "shared_structural_edges": 2,
     "lump_threshold": 0.6,
-    "unresearched_mechanism_records": 278,
+    "unresearched_mechanism_records": 279,
     "actions": {
       "DROP_NON_MECHANISM": 109,
       "DROP_DEPRECATED": 20,
       "DROP_GROUPING_TERM": 0,
       "LUMP_INTO_PARENT": 0,
       "CURATE_ROOT_WITH_SUBTYPES": 4,
-      "ADD_CANONICAL_EXAMPLES": 92,
+      "ADD_CANONICAL_EXAMPLES": 93,
       "BUILD_CAUSAL_GRAPH": 119,
       "DEEPEN_CAUSAL_GRAPH": 195,
       "ALREADY_DEEP": 59,
@@ -2044,6 +2044,29 @@
         "no canonical_examples +30"
       ]
     },
+    {
+      "identifier": "traitmech:000361",
+      "label": "Gao-Her-DUF system",
+      "category": "genomics",
+      "slug": "gao_her_duf_system",
+      "score": 42.0,
+      "action": "ADD_CANONICAL_EXAMPLES",
+      "edges": 3,
+      "nodes": 4,
+      "components": 1,
+      "orphans": 0,
+      "examples": 0,
+      "canonical_examples_reviewed_empty": false,
+      "children": 0,
+      "series": null,
+      "series_size": 0,
+      "series_overlap": null,
+      "researched": false,
+      "reasons": [
+        "thin graph (3 edges) +12",
+        "no canonical_examples +30"
+      ]
+    },
     {
       "identifier": "traitmech:000353",
       "label": "Gao-Hhe system",
@@ -6302,7 +6325,7 @@
       "orphans": 0,
       "examples": 1,
       "canonical_examples_reviewed_empty": false,
-      "children": 115,
+      "children": 116,
       "series": null,
       "series_size": 0,
       "series_overlap": null,

app/discussions/data.js

@@ -1577,6 +1577,25 @@ window.searchData = [
   "posed_by": "codex",
   "page_url": "../../pages/traits/genomics/gao_ape_system.html#apea-trigger-and-homolog-scope-gap"
  },
+ {
+  "discussion_id": "gao-her-duf-mechanism-gap",
+  "prompt": "Resolve Gao_Her_DUF natural hosts, DUF4297/HerA_DUF component functions, phage triggers, and effector activity before minting narrower Gao_Her_DUF mechanism children.",
+  "kind": "KNOWLEDGE_GAP",
+  "status": "OPEN",
+  "is_gap": "Knowledge gap",
+  "source_name": "Gao-Her-DUF system",
+  "source_id": "traitmech:000361",
+  "source_file": "gao_her_duf_system.yaml",
+  "attaches_to": [
+   "causal_graphs#gao_her_duf_locus_restricts_phage"
+  ],
+  "rationale": "Gao et al. support widespread antiviral gene cassettes that mediate protection against specific bacteriophages, and DefenseFinder models Gao_Her_DUF as a two-profile system under the Gao_Her family key. The exact natural host breadth, DUF4297/HerA_DUF component identities, phage trigger, and profile-to-activity mapping remain unresolved.",
+  "num_experiments": 0,
+  "num_evidence": 0,
+  "evidence_refs": [],
+  "posed_by": "codex",
+  "page_url": "../../pages/traits/genomics/gao_her_duf_system.html#gao-her-duf-mechanism-gap"
+ },
  {
   "discussion_id": "gao-hhe-mechanism-gap",
   "prompt": "Resolve Gao_Hhe natural hosts, HheA component function, phage triggers, and effector activity before minting narrower Gao_Hhe mechanism children.",
@@ -4220,9 +4239,9 @@ window.searchData = [
  }
 ];
 window.searchMetrics = {
- "total_discussions": 230,
- "total_knowledge_gaps": 148,
- "total_source_entries": 228,
+ "total_discussions": 231,
+ "total_knowledge_gaps": 149,
+ "total_source_entries": 229,
  "kinds": [
   "CONTROVERSY",
   "CURATION_TODO",

data/traits/genomics/gao_her_duf_system.yaml

@@ -0,0 +1,159 @@
+identifier: traitmech:000361
+label: Gao-Her-DUF system
+definition: A phage defense system in which an organism possesses a Gao_Her_DUF locus
+  represented by DefenseFinder as a two-profile model requiring Gao_Her_DUF__DUF4297
+  and Gao_Her_DUF__HerA_DUF.
+definition_source: DOI:10.1126/science.aba0372
+trait_category: GENOMICS
+term_kind: CLASS
+mapping_status: PROPOSED
+parent_traits:
+- traitmech:000209
+synonyms:
+- synonym_text: Gao_Her_DUF
+  synonym_type: RELATED_SYNONYM
+  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
+- synonym_text: Gao_Her_DUF__DUF4297
+  synonym_type: RELATED_SYNONYM
+  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+- synonym_text: Gao_Her_DUF__HerA_DUF
+  synonym_type: RELATED_SYNONYM
+  source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+evidence:
+- reference: PMID:32855333
+  snippet: By systematic defense gene prediction and heterologous reconstitution,
+    here we discover 29 widespread antiviral gene cassettes, collectively present
+    in 32% of all sequenced bacterial and archaeal genomes, that mediate protection
+    against specific bacteriophages.
+  notes: Gao et al. support a systematic defense-gene prediction and heterologous
+    reconstitution campaign that discovered widespread antiviral gene cassettes.
+- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
+  snippet: Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate
+    antiviral immunity in prokaryotes
+  notes: The DefenseFinder article registry maps the broader Gao_Her family key to
+    the Gao et al. prokaryotic antiviral-immunity paper.
+- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
+  snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF"
+  notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile system
+    requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
+- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+  snippet: '| Gao_Her_DUF__DUF4297                             | Gao_Her_DUF__DUF4297                             |
+    Gao_Her_DUF            | Custom                  | 20     |'
+  notes: The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF.
+- reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+  snippet: '| Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF__HerA_DUF                            |
+    Gao_Her_DUF            | Custom                  | 20     |'
+  notes: The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF.
+causal_graphs:
+- graph_id: gao_her_duf_locus_restricts_phage
+  title: Gao-Her-DUF loci confer bacterial phage defense
+  description: Conservative system-level sketch linking possession of a Gao_Her_DUF
+    locus to Gao et al. antiviral cassette defense without asserting the unresolved
+    Her-DUF component activities.
+  scope_status: NONMECHANISTIC
+  scope_notes: The graph captures Gao-Her-DUF as a named DefenseFinder two-profile
+    Gao-family system while leaving natural hosts, DUF4297/HerA_DUF protein functions,
+    phage triggers, and direct effector activity unresolved.
+  nodes:
+  - node_id: gao_her_duf_locus
+    label: Gao_Her_DUF locus
+    node_type: GENETIC_ELEMENT
+    description: A DefenseFinder Gao_Her_DUF phage-defense locus represented by custom
+      DUF4297 and HerA_DUF profiles.
+  - node_id: gao_2020_antiviral_cassette_defense
+    label: Gao 2020 antiviral cassette defense
+    node_type: BIOLOGICAL_PROCESS
+    description: Bacteriophage protection by one of the antiviral gene cassettes described
+      in the Gao et al. systematic defense-gene discovery campaign.
+  - node_id: gao_her_duf_system_trait
+    label: Gao-Her-DUF system
+    node_type: TRAIT
+    grounding: traitmech:000361
+    description: Possession of a genome-encoded Gao-Her-DUF phage-defense system.
+  - node_id: phage_defense_system
+    label: phage defense system
+    node_type: TRAIT
+    grounding: traitmech:000209
+    description: Possession of one or more genome-encoded immune systems that inhibit
+      bacteriophage infection.
+  edges:
+  - subject: gao_her_duf_locus
+    predicate: contributes to
+    predicate_id: RO:0002326
+    object: gao_2020_antiviral_cassette_defense
+    description: DefenseFinder maps the broader Gao_Her family key to the Gao et al.
+      systematic antiphage-system discovery paper and models Gao_Her_DUF as a two-profile
+      system requiring DUF4297 and HerA_DUF.
+    evidence:
+    - reference: PMID:32855333
+      snippet: By systematic defense gene prediction and heterologous reconstitution,
+        here we discover 29 widespread antiviral gene cassettes, collectively present
+        in 32% of all sequenced bacterial and archaeal genomes, that mediate protection
+        against specific bacteriophages.
+      notes: Gao et al. support bacteriophage protection by widespread antiviral gene
+        cassettes.
+    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
+      snippet: Gao_Her | 10\.1126/science\.aba0372 | Diverse enzymatic activities
+        mediate antiviral immunity in prokaryotes
+      notes: The DefenseFinder article registry maps the broader Gao_Her family key
+        to the Gao et al. prokaryotic antiviral-immunity paper.
+    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
+      snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF"
+      notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile system
+        requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
+    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+      snippet: '| Gao_Her_DUF__DUF4297                             | Gao_Her_DUF__DUF4297                             |
+        Gao_Her_DUF            | Custom                  | 20     |'
+      notes: The DefenseFinder HMM inventory records Gao_Her_DUF__DUF4297 under Gao_Her_DUF.
+    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
+      snippet: '| Gao_Her_DUF__HerA_DUF                            | Gao_Her_DUF__HerA_DUF                            |
+        Gao_Her_DUF            | Custom                  | 20     |'
+      notes: The DefenseFinder HMM inventory records Gao_Her_DUF__HerA_DUF under Gao_Her_DUF.
+  - subject: gao_2020_antiviral_cassette_defense
+    predicate: confers
+    predicate_id: METPO:2007700
+    object: gao_her_duf_system_trait
+    description: Gao_Her_DUF-associated antiviral cassette defense realizes the Gao-Her-DUF
+      system trait.
+    evidence:
+    - reference: PMID:32855333
+      snippet: By systematic defense gene prediction and heterologous reconstitution,
+        here we discover 29 widespread antiviral gene cassettes, collectively present
+        in 32% of all sequenced bacterial and archaeal genomes, that mediate protection
+        against specific bacteriophages.
+      notes: Gao et al. support bacteriophage protection by widespread antiviral gene
+        cassettes.
+  - subject: gao_her_duf_system_trait
+    predicate: is a
+    predicate_id: rdfs:subClassOf
+    object: phage_defense_system
+    description: Gao-Her-DUF system possession is a phage-defense-system trait.
+    evidence:
+    - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
+      snippet: "Gao_Her\tGao_Her_DUF\t2\t2\tGao_Her_DUF__DUF4297, Gao_Her_DUF__HerA_DUF"
+      notes: The DefenseFinder rules table models Gao_Her_DUF as a two-profile system
+        requiring Gao_Her_DUF__DUF4297 and Gao_Her_DUF__HerA_DUF.
+discussions:
+- discussion_id: gao-her-duf-mechanism-gap
+  prompt: Resolve Gao_Her_DUF natural hosts, DUF4297/HerA_DUF component functions,
+    phage triggers, and effector activity before minting narrower Gao_Her_DUF mechanism
+    children.
+  kind: KNOWLEDGE_GAP
+  status: OPEN
+  rationale: Gao et al. support widespread antiviral gene cassettes that mediate protection
+    against specific bacteriophages, and DefenseFinder models Gao_Her_DUF as a two-profile
+    system under the Gao_Her family key. The exact natural host breadth, DUF4297/HerA_DUF
+    component identities, phage trigger, and profile-to-activity mapping remain unresolved.
+  attaches_to:
+  - causal_graphs#gao_her_duf_locus_restricts_phage
+  posed_by: codex
+  posed_date: '2026-09-22'
+curation_history:
+- timestamp: '2026-09-22T09:33:34Z'
+  curator: codex
+  action: MINTED_TRAITMECH_ID
+  changes: Minted Gao-Her-DUF system as a DOI-backed GENOMICS TraitRecord under phage
+    defense system after an ignored-and-hidden duplicate review found no exact live
+    TraitMech, METPO, history, or prior proposal record; the replacement placeholder
+    is reserved in proposals/metpo_traitmech_v238.
+  llm_assisted: true

history/records/gao_her_duf_system/2026-09-22T093443Z-codex-da0d31.yaml

@@ -0,0 +1,25 @@
+history_version: 1
+target:
+  kind: record
+  path: data/traits/genomics/gao_her_duf_system.yaml
+  slug: gao_her_duf_system
+session:
+  id: 2026-09-22T093443Z-codex-da0d31
+  timestamp: '2026-09-22T09:34:43Z'
+  actors:
+  - type: ai_agent
+    name: codex
+    model: gpt-5
+    agent_tool: codex
+events:
+- type: CREATE
+  outcome: changed
+  sections:
+  - identity
+  - evidence
+  - causal_graphs
+  summary: Add Gao-Her-DUF phage-defense system trait
+  details: Added traitmech:000361 for the DefenseFinder Gao_Her_DUF two-profile phage-defense
+    subsystem, reserved METPO:1031500 in proposals/metpo_traitmech_v238, recorded Gao et al.
+    and pinned DefenseFinder article/rules/HMM evidence, and opened a mechanism-gap discussion
+    for unresolved Her-DUF host, trigger, and effector details.

pages/browse.html

@@ -23,7 +23,7 @@
 <header>
   <p class="breadcrumb"><a href="index.html">TraitMech</a> <span>›</span> Record browser</p>
   <h1>Record browser</h1>
-  <p class="tagline">Browse 755 trait records across 10 categories.
+  <p class="tagline">Browse 756 trait records across 10 categories.
     Each record carries METPO provenance, causal graphs, kg-microbe matches, and nearest neighbors.</p>
 </header>
 
@@ -39,7 +39,7 @@ <h3>METABOLISM</h3>
 
     <a class="card cat-tile" href="category/genomics.html">
       <h3>GENOMICS</h3>
-      <p class="big">171</p>
+      <p class="big">172</p>
       <p class="meta">19 with embedding</p>
     </a>
 
@@ -109,10 +109,10 @@ <h3>QUANTITATIVE_PROPERTY</h3>
       <a href="https://bioportal.bioontology.org/ontologies/METPO">METPO</a>
     </div>
     <div>
-      Corpus as of 2026-09-22 09:00 UTC from
+      Corpus as of 2026-09-22 09:33 UTC from
       <a href="https://w3id.org/metpo">METPO 2026-06-12</a>
-      · 755 TraitRecords
-      · embedding coverage 63.2%
+      · 756 TraitRecords
+      · embedding coverage 63.1%
       (kg-microbe deepwalk 512-D, 2026-04-25)
     </div>
   </div>

pages/category/ecology.html

@@ -256,10 +256,10 @@ <h1>ECOLOGY <span class="meta">(26)</span></h1>
       <a href="https://bioportal.bioontology.org/ontologies/METPO">METPO</a>
     </div>
     <div>
-      Corpus as of 2026-09-22 09:00 UTC from
+      Corpus as of 2026-09-22 09:33 UTC from
       <a href="https://w3id.org/metpo">METPO 2026-06-12</a>
-      · 755 TraitRecords
-      · embedding coverage 63.2%
+      · 756 TraitRecords
+      · embedding coverage 63.1%
       (kg-microbe deepwalk 512-D, 2026-04-25)
     </div>
   </div>